Low conservation and species-specific evolution of alternative splicing in humans and mice: Comparative genomics analysis using well-annotated full-length cDNAs

Jun Ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Masahide Seki, Takuma Irie, Nono Takeuchi, Takuya Ueda, Mitsuteru Nakao, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi

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21 Citations (Scopus)

Abstract

Using full-length cDNA sequences, we compared alternative splicing (AS) in humans and mice. The alignment of the human and mouse genomes showed that 86% of 199 426 total exons in human AS variants were conserved in the mouse genome. Of the 20 392 total human AS variants, however, 59% consisted of all conserved exons. Comparing AS patterns between human and mouse transcripts revealed that only 431 transcripts from 189 loci were perfectly conserved AS variants. To exclude the possibility that the full-length human cDNAs used in the present study, especially those with retained introns, were cloning artefacts or prematurely spliced transcripts, we experimentally validated 34 such cases. Our results indicate that even retained-intron type transcripts are typically expressed in a highly controlled manner and interact with translating ribosomes. We found non-conserved AS exons to be predominantly outside the coding sequences (CDSs). This suggests that non-conserved exons in the CDSs of transcripts cause functional constraint. These findings should enhance our understanding of the relationship between AS and species specificity of human genes.

Original languageEnglish
Pages (from-to)6386-6395
Number of pages10
JournalNucleic acids research
Volume36
Issue number20
DOIs
Publication statusPublished - 2008 Nov 28

ASJC Scopus subject areas

  • Genetics

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    Takeda, J. I., Suzuki, Y., Sakate, R., Sato, Y., Seki, M., Irie, T., Takeuchi, N., Ueda, T., Nakao, M., Sugano, S., Gojobori, T., & Imanishi, T. (2008). Low conservation and species-specific evolution of alternative splicing in humans and mice: Comparative genomics analysis using well-annotated full-length cDNAs. Nucleic acids research, 36(20), 6386-6395. https://doi.org/10.1093/nar/gkn677